Ebola Outbreak Strains Sequenced

Ninety-nine publicly available genomes could help researchers working to develop diagnostics, vaccines, and therapies.

By Tracy Vence | August 28, 2014

Augustine Goba of Kenema Government Hospital diagnosed the first case of Ebola in Sierra Leone.STEPHEN GIRE

An international team led by investigators at Harvard University has sequenced 99 Ebola virus genomes isolated from the blood of 78 patients in Sierra Leone—one of four countries at the center of the largest-ever Ebola outbreak. Within these sequences, which were each made public within a matter of days post-assembly, the researchers found evidence of the rapid accumulation of mutations affecting biologically meaningful targets, which could have implications for the development of diagnostics, vaccines, and therapies. The team’s analysis of all 99 genomes was published today (August 28) in Science.

“This analysis will provide the backbone for tracking the virus as it spreads, and to see if future outbreaks outside of these countries are connected both epidemiologically and genetically,” emerging infectious diseases researcher Matthew Frieman from the University of Maryland School of Medicine who was not involved in the work told The Scientist in an e-mail. “The ability to deep sequence virus samples rapidly, inexpensively, and safely has opened up a window in to genomic surveillance that did not exist before.”

Harvard’s Pardis Sabeti and her colleagues have been working to detect signs of natural selection in the Ebola virus genome for the last five years. With the help of collaborators from Tulane University Medical Center, other US institutions, and hospitals in Sierra Leone and Nigeria, Sabeti’s team had already established biosecurity level-4 diagnostic testing infrastructure in West Africa before the first signs of an Ebola outbreak emerged in Guinea this February. In March, study coauthors Stephen Gire and Kristian Andersen traveled to Sierra Leone and, along with coauthor Augustine Goba from the country’s Kenema Government Hospital, began testing patients for Ebola.

“In May, they had our first positive case,” said Sabeti. “When that happened, we moved very quickly.”

Once cleared by the Sierra Leonean health ministry, Gire, Andersen, Goba, and their colleagues began shipping patient samples to the Broad Institute in Cambridge, Massachusetts, where Sabeti is a senior associate member. The Broad team sequenced each sample six times at about 2,000x coverage.

“This dataset allowed the authors to provide a detailed and unprecedented account of the evolution and spread of Ebola virus within Sierra Leone during a portion of the ongoing epidemic,” Jason Ladner from the US Army Medical Research Institute of Infectious Diseases in Fort Detrick, Maryland, wrote in an e-mail to The Scientist. “In particular, these sequences have provided the first look into how the virus has been changing since the start of the outbreak. Such genetic changes are important to account for in the design and testing of medical countermeasures.”

Shortly after completing the sequencing work, Sabeti and her colleagues made the results publicly available online, and almost immediately they began receiving calls from researchers working to develop diagnostics, vaccines, and therapies. “We wanted as many eyes looking at the data as quickly as possible,” said Sabeti. “Already we’ve seen that the virus has mutated away from currently used diagnostics, [which] is likely to have some effect on the sensitivity of those assays.”

Specifically, the team’s analysis suggested that the Ebola virus strain circulating in West Africa diverged from Middle African lineages around 2004, and has since shown sustained human-to-human transmission. While the researchers were unable to pinpoint the original animal source of the virus, they did not find any evidence of additional zoonotic sources in the outbreak strains.

“The organism is changing all the time and that can create problems,” said University of Warwick microbial genomicist Mark Pallen. To devise effective countermeasures, he added, “you need to be clear which parts of the genome are staying fairly static.”

“This sequence analysis lets us know where it [the virus] went and gives scientists a scaffold to look for where it came from,” added Frieman.

The World Health Organization (WHO), which earlier this month declared the ongoing epidemic a Public Health Emergency of International Concern, today (August 28) said that nearly 20,000 people could be infected with Ebola before the outbreak is contained. According to the WHO, at least 3,069 people have been infected with the virus to date; 1,552 have died.

“We’ve been really overwhelmed by what’s going on,” said Sabeti. “This is an extraordinary emergency on an unprecedented scale.”

Five healthcare workers who assisted the team on the ground in Sierra Leone died of Ebola. All five were infected with the virus while caring for sick patients or family members, Sabeti said. In their paper, the authors honored their deceased colleagues—five would-be coauthors on the work—who gave their lives to help others.

Just to be correct about the issue of mutations - specifically the point that "the researchers found evidence of the rapid accumulation of mutations affecting biologically meaningful targets, " It is important to consider the data in a couple ways. First of all, I don't think anyone would claim this necessarily is "rapid" but is a common feature for genomes of viruses and bacteria that grow up in large numbers, allowing for spontaneous mutations to occur and accumulate in the population. Mutations can occur and persist, and if they are not selected against, become part of the variation of the genome. That brings up a second point. If all the viruses that were sequenced caused death to a human patient, then the mutations are meaningful in that they quite possibly identify parts that can accept a particular change and not affect infectivity. In other words, they identify "unimportant" parts. I hestitate to leave it at that because it may turn of that sites of change in the genome actually are important and can only accept certain changes and still function. That's why it is not sensible that conclusions are drawn from so few numbers of sequenced genomes. Ninety-nine sequences are not enough to drawn those conclusions. Having the sequence is enormously important for diagnosis and for providing a starting point for developing a vaccine and therapy. There is little question this is extremely valueable information to have but it is equally important to appreciate what it means and what it doesn't.

I am nothing but an electronics engineer. But I've worked most of my life on advanced medical instrumentation. That includes assisting Dr. Kary Mullis in developing the initial DNA analysis methods (PCR) in order to detect HIV in the blood banking system.

Papers like this bother me since they do not tell the entire story. I do not pretend to be a epidemioligist or a specialist in RNA analysis.

But the papers I've read that talk of rapid mutating strike me as being a bit irresponsible. It appears to be as if the main sequence of the disease remains more or less stable. And like all open ended RNA additional sequences glue themselves on the end. If indeed there were signicant mutations wouldn't we expect to see disease symptoms changing rapidly as well? And we should also add that mutations may inactivate the virus as easily as making it more virulent.

I am also having a bit of trouble with people treating a disease that COULD (but which we haven't been able to verify) be spread through sputum or vomitus aerosols in almost direct contact as making it "airborne". I see that as an irresponsible redefinition of the word "airborne" when applied to a disease.